rs3956418

chr1-83363674-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.673 in 152,012 control chromosomes in the GnomAD database, including 34,973 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34973 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102158 AN: 151894 Hom.: 34923 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.642

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.673 AC: 102264 AN: 152012 Hom.: 34973 Cov.: 33 AF XY: 0.673 AC XY: 50042 AN XY: 74318

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.642

Alfa AF: 0.624 Hom.: 13635

Bravo AF: 0.679

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	7.7
Dann	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3956418; hg19: chr1-83829357;